Matter, Energy, and the Spirit

In #religion

Theists seem to critique naturalism with the claim that there is more to the universe than just "matter and energy". However, even physicists have in their models certain entities which cannot be categorized as either matter or energy. The quantum wavefunction is one clear example. There is also a history of introducing entities into models which later turn out to be unnecessary - "Vis viva" (i.e. life force), "phlogiston" (i.e. heat fluid), and "celestial matter" (vs terrestial matter). It is not that scientists are dogmatically against such entities, it's just that they should be dropped when they don't explain and predict anything or alternative explanations are simpler and more direct. We don't use agency to explain the motion of the planets anymore, for example, but we once did.

There are other entities in models which serve as placeholders for the unknown, for example "dark matter". No one seriously thinks labeling the gravitational effect observed from galactic rotation curves is better understood once we label it "dark matter". It is just a placeholder, until we figure out what dark matter actually is - neutrinos, black holes, altered gravitation on large scale, etc...

Given this backdrop, what explanative and predictive power do the terms "spirit" and "supernatural agency" have anymore? Can we name anything that we understand better with their inclusion than we do without? What direct observations make these entities useful in any model of the universe, beyond as a placeholder for the unknown?